Contacts of the strand formed by residues 89 - 94 (chain M) in PDB entry 7K63


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with ASP 89 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41M  THR*     6.2     1.8    -      -       +      -
     42M  CYS      3.7     4.5    -      -       -      +
     43M  LYS*     4.6    12.1    -      -       +      +
     85M  GLY*     3.2    13.7    -      -       -      -
     86M  SER      3.0    27.7    +      -       -      +
     88M  GLN*     1.3    80.0    +      -       -      +
     90M  PHE*     1.3    62.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 90 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41M  THR*     3.6     6.8    -      -       -      +
     42M  CYS*     2.8    40.1    +      -       +      +
     44M  ALA*     4.6     2.2    -      -       +      -
     48M  ILE*     3.5    37.5    -      -       +      -
     50M  SER*     3.9     8.5    -      -       -      -
     52M  LEU*     3.5    34.8    -      -       +      -
     54M  TRP*     4.5     1.8    -      -       +      +
     70M  ALA*     3.5    33.4    -      -       +      -
     84M  SER      3.8     6.3    -      -       -      +
     85M  GLY*     3.7    14.8    -      -       -      -
     86M  SER*     3.8     3.1    -      -       -      -
     87M  GLY      3.9    14.8    -      -       -      -
     88M  GLN*     3.6    25.1    -      -       -      -
     89M  ASP*     1.3    76.7    -      -       -      +
     91M  SER*     1.3    64.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 91 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39M  THR*     4.4    16.2    -      -       -      -
     40M  ILE      3.2     9.9    -      -       -      -
     41M  THR*     4.8     4.5    -      -       -      -
     54M  TRP*     3.9    11.7    +      -       -      -
     70M  ALA      4.9     0.2    -      -       -      +
     83M  GLY*     3.2    20.5    -      -       -      -
     84M  SER*     2.7    34.3    +      -       -      +
     90M  PHE*     1.3    81.1    -      -       -      +
     92M  LEU*     1.3    61.2    +      -       -      +
     93M  THR*     4.6     5.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 92 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38M  VAL      3.8     0.4    -      -       -      +
     39M  THR*     3.1     6.8    -      -       -      +
     40M  ILE*     2.6    60.5    +      -       +      +
     54M  TRP*     3.6    42.0    -      -       +      -
     66M  LEU*     4.8     3.1    -      -       +      -
     67M  ILE*     3.5    32.1    -      -       +      -
     81M  PHE*     4.9     8.3    -      -       +      -
     82M  SER      3.7     0.7    -      -       -      +
     91M  SER*     1.3    72.8    -      -       -      +
     93M  THR*     1.3    71.3    +      -       -      +
     94M  ILE*     4.6     7.6    -      -       +      -
    105M  TYR*     3.7    33.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 93 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37M  ARG*     3.8    29.6    -      -       +      -
     38M  VAL      3.3     6.3    -      -       -      +
     39M  THR*     4.0    12.4    +      -       -      +
     80M  ARG      3.4     1.2    -      -       -      +
     81M  PHE*     3.3     5.7    -      -       -      +
     82M  SER*     2.6    57.6    +      -       -      +
     83M  GLY*     5.4     0.5    -      -       -      -
     91M  SER*     4.6     6.8    +      -       -      -
     92M  LEU*     1.3    79.4    +      -       -      +
     94M  ILE*     1.3    67.0    +      -       -      +
     95M  ASN*     4.0    10.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 94 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36M  GLU      4.0     1.4    -      -       -      +
     37M  ARG*     3.2     3.1    -      -       -      +
     38M  VAL*     2.8    44.3    +      -       +      +
     40M  ILE*     4.9     3.6    -      -       +      -
     80M  ARG*     3.6    30.7    -      -       -      +
     81M  PHE*     3.5    24.5    -      -       +      -
     92M  LEU*     4.6    10.1    -      -       +      -
     93M  THR*     1.3    77.6    -      -       -      +
     95M  ASN*     1.3    60.9    +      -       -      +
     96M  ASN      4.7     0.7    -      -       -      +
     97M  LEU*     3.6    15.5    -      -       +      -
    101M  ASP*     3.6     9.9    -      -       -      +
    105M  TYR*     3.7    32.8    -      -       +      +
    123M  LEU*     3.9    21.1    -      -       +      -
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il